257 lines
7.0 KiB
C++
257 lines
7.0 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "compute_dihedral_local.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "domain.h"
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#include "force.h"
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#include "dihedral.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute dihedral/local command");
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if (atom->avec->dihedrals_allow == 0)
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error->all("Compute dihedral/local used when dihedrals are not allowed");
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local_flag = 1;
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nvalues = narg - 3;
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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pflag = -1;
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nvalues = 0;
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int i;
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for (int iarg = 3; iarg < narg; iarg++) {
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i = iarg-3;
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if (strcmp(arg[iarg],"phi") == 0) pflag = nvalues++;
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else error->all("Invalid keyword in compute dihedral/local command");
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}
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nmax = 0;
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vector = NULL;
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array = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeDihedralLocal::~ComputeDihedralLocal()
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{
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memory->sfree(vector);
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memory->destroy_2d_double_array(array);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDihedralLocal::init()
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{
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if (force->dihedral == NULL)
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error->all("No dihedral style is defined for compute dihedral/local");
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// do initial memory allocation so that memory_usage() is correct
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ncount = compute_dihedrals(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDihedralLocal::compute_local()
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{
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invoked_local = update->ntimestep;
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// count local entries and compute dihedral info
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ncount = compute_dihedrals(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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ncount = compute_dihedrals(1);
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}
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/* ----------------------------------------------------------------------
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count dihedrals on this proc
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only count if 2nd atom is the one storing the dihedral
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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if flag is set, compute requested info about dihedral
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------------------------------------------------------------------------- */
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int ComputeDihedralLocal::compute_dihedrals(int flag)
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{
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int i,m,n,atom1,atom2,atom3,atom4;
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double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
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double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
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double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
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double c2mag,sin2,sc1,sc2,s1,s2,s12,c;
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double *pbuf;
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double **x = atom->x;
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_atom1 = atom->dihedral_atom1;
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int **dihedral_atom2 = atom->dihedral_atom2;
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int **dihedral_atom3 = atom->dihedral_atom3;
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int **dihedral_atom4 = atom->dihedral_atom4;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (flag) {
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if (nvalues == 1) {
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if (pflag >= 0) pbuf = vector;
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} else {
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if (pflag >= 0) pbuf = &array[0][pflag];
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}
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}
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double PI = 4.0*atan(1.0);
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m = n = 0;
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for (atom2 = 0; atom2 < nlocal; atom2++) {
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if (!(mask[atom2] & groupbit)) continue;
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for (i = 0; i < num_dihedral[atom2]; i++) {
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if (tag[atom2] != dihedral_atom2[atom2][i]) continue;
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atom1 = atom->map(dihedral_atom1[atom2][i]);
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if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
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atom3 = atom->map(dihedral_atom3[atom2][i]);
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if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
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atom4 = atom->map(dihedral_atom4[atom2][i]);
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if (atom4 < 0 || !(mask[atom4] & groupbit)) continue;
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if (flag) {
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// phi calculation from dihedral style OPLS
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if (pflag >= 0) {
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vb1x = x[atom1][0] - x[atom2][0];
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vb1y = x[atom1][1] - x[atom2][1];
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vb1z = x[atom1][2] - x[atom2][2];
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domain->minimum_image(vb1x,vb1y,vb1z);
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vb2x = x[atom3][0] - x[atom2][0];
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vb2y = x[atom3][1] - x[atom2][1];
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vb2z = x[atom3][2] - x[atom2][2];
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domain->minimum_image(vb2x,vb2y,vb2z);
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vb2xm = -vb2x;
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vb2ym = -vb2y;
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vb2zm = -vb2z;
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domain->minimum_image(vb2xm,vb2ym,vb2zm);
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vb3x = x[atom4][0] - x[atom3][0];
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vb3y = x[atom4][1] - x[atom3][1];
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vb3z = x[atom4][2] - x[atom3][2];
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domain->minimum_image(vb3x,vb3y,vb3z);
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sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
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sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
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sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
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rb1 = sqrt(sb1);
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rb3 = sqrt(sb3);
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c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
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b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
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b1mag = sqrt(b1mag2);
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b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
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b2mag = sqrt(b2mag2);
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b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
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b3mag = sqrt(b3mag2);
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ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
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r12c1 = 1.0 / (b1mag*b2mag);
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c1mag = ctmp * r12c1;
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ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
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r12c2 = 1.0 / (b2mag*b3mag);
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c2mag = ctmp * r12c2;
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sin2 = MAX(1.0 - c1mag*c1mag,0.0);
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sc1 = sqrt(sin2);
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if (sc1 < SMALL) sc1 = SMALL;
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sc1 = 1.0/sc1;
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sin2 = MAX(1.0 - c2mag*c2mag,0.0);
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sc2 = sqrt(sin2);
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if (sc2 < SMALL) sc2 = SMALL;
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sc2 = 1.0/sc2;
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s1 = sc1 * sc1;
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s2 = sc2 * sc2;
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s12 = sc1 * sc2;
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c = (c0 + c1mag*c2mag) * s12;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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pbuf[n] = 180.0*acos(c)/PI;
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}
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n += nvalues;
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}
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m++;
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDihedralLocal::reallocate(int n)
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{
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// grow vector or array and indices array
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while (nmax < n) nmax += DELTA;
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if (nvalues == 1) {
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memory->sfree(vector);
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vector = (double *) memory->smalloc(nmax*sizeof(double),
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"bond/local:vector");
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vector_local = vector;
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} else {
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memory->destroy_2d_double_array(array);
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array = memory->create_2d_double_array(nmax,nvalues,
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"bond/local:array");
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array_local = array;
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeDihedralLocal::memory_usage()
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{
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double bytes = nmax*nvalues * sizeof(double);
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return bytes;
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}
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